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<h1> Representation and manipulation of genomic intervals
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</div><h2>Documentation for package &lsquo;GenomicRanges&rsquo; version 1.8.13</h2>

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<h2><a name="A">-- A --</a></h2>

<table width="100%">
<tr><td width="25%"><a href="GRanges-class.html">as.data.frame-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">as.data.frame-method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">as.data.frame-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">as.data.frame-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">assay</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">assay-method</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">assay&lt;-</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">assay&lt;--method</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">assays</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">assays-method</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">assays&lt;-</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">assays&lt;--method</a></td>
<td>SummarizedExperiment instances</td></tr>
</table>

<h2><a name="C">-- C --</a></h2>

<table width="100%">
<tr><td width="25%"><a href="GRanges-class.html">c-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">c-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="constraint.html">checkConstraint</a></td>
<td>Enforcing constraints thru Constraint objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">cigar</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">cigar-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="cigar-utils.html">cigar-utils</a></td>
<td>CIGAR utility functions</td></tr>
<tr><td width="25%"><a href="cigar-utils.html">cigarNarrow</a></td>
<td>CIGAR utility functions</td></tr>
<tr><td width="25%"><a href="cigar-utils.html">cigarOpTable</a></td>
<td>CIGAR utility functions</td></tr>
<tr><td width="25%"><a href="cigar-utils.html">cigarQNarrow</a></td>
<td>CIGAR utility functions</td></tr>
<tr><td width="25%"><a href="cigar-utils.html">cigarToCigarTable</a></td>
<td>CIGAR utility functions</td></tr>
<tr><td width="25%"><a href="cigar-utils.html">cigarToIRanges</a></td>
<td>CIGAR utility functions</td></tr>
<tr><td width="25%"><a href="cigar-utils.html">cigarToIRangesListByAlignment</a></td>
<td>CIGAR utility functions</td></tr>
<tr><td width="25%"><a href="cigar-utils.html">cigarToIRangesListByRName</a></td>
<td>CIGAR utility functions</td></tr>
<tr><td width="25%"><a href="cigar-utils.html">cigarToQWidth</a></td>
<td>CIGAR utility functions</td></tr>
<tr><td width="25%"><a href="cigar-utils.html">cigarToRleList</a></td>
<td>CIGAR utility functions</td></tr>
<tr><td width="25%"><a href="cigar-utils.html">cigarToWidth</a></td>
<td>CIGAR utility functions</td></tr>
<tr><td width="25%"><a href="constraint.html">class:Constraint</a></td>
<td>Enforcing constraints thru Constraint objects</td></tr>
<tr><td width="25%"><a href="constraint.html">class:ConstraintORNULL</a></td>
<td>Enforcing constraints thru Constraint objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">class:GappedAlignmentPairs</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">class:GappedAlignments</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">class:GenomicRanges</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GenomicRangesList-class.html">class:GenomicRangesList</a></td>
<td>GenomicRangesList objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">class:GRanges</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">class:GRangesList</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">class:Seqinfo</a></td>
<td>Seqinfo objects</td></tr>
<tr><td width="25%"><a href="GenomicRangesList-class.html">class:SimpleGenomicRangesList</a></td>
<td>GenomicRangesList objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">coerce-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">coerce-method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">coerce-method</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">coerce-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GenomicRangesList-class.html">coerce-method</a></td>
<td>GenomicRangesList objects</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">coerce-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td width="25%"><a href="map-methods.html">coerce-method</a></td>
<td>Mapping ranges between sequences</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">colData</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">colData-method</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">colData&lt;-</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">colData&lt;--method</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="GenomicRanges-comparison.html">compare-method</a></td>
<td>Comparing and ordering genomic ranges</td></tr>
<tr><td width="25%"><a href="constraint.html">Constraint</a></td>
<td>Enforcing constraints thru Constraint objects</td></tr>
<tr><td width="25%"><a href="constraint.html">constraint</a></td>
<td>Enforcing constraints thru Constraint objects</td></tr>
<tr><td width="25%"><a href="constraint.html">Constraint-class</a></td>
<td>Enforcing constraints thru Constraint objects</td></tr>
<tr><td width="25%"><a href="constraint.html">constraint&lt;-</a></td>
<td>Enforcing constraints thru Constraint objects</td></tr>
<tr><td width="25%"><a href="constraint.html">ConstraintORNULL</a></td>
<td>Enforcing constraints thru Constraint objects</td></tr>
<tr><td width="25%"><a href="constraint.html">ConstraintORNULL-class</a></td>
<td>Enforcing constraints thru Constraint objects</td></tr>
<tr><td width="25%"><a href="constraint.html">Constraints</a></td>
<td>Enforcing constraints thru Constraint objects</td></tr>
<tr><td width="25%"><a href="countGenomicOverlaps.html">countGenomicOverlaps</a></td>
<td>Count Read Hits in Genomic Features</td></tr>
<tr><td width="25%"><a href="countGenomicOverlaps.html">countGenomicOverlaps-method</a></td>
<td>Count Read Hits in Genomic Features</td></tr>
<tr><td width="25%"><a href="findOverlaps-methods.html">countOverlaps-method</a></td>
<td>GRanges, GRangesList, GappedAlignments and GappedAlignmentPairs Interval Overlaps</td></tr>
<tr><td width="25%"><a href="coverage-methods.html">coverage-method</a></td>
<td>Coverage of a GRanges, GRangesList, GappedAlignments, or GappedAlignmentPairs object</td></tr>
<tr><td width="25%"><a href="coverage-methods.html">coverage-methods</a></td>
<td>Coverage of a GRanges, GRangesList, GappedAlignments, or GappedAlignmentPairs object</td></tr>
</table>

<h2><a name="D">-- D --</a></h2>

<table width="100%">
<tr><td width="25%"><a href="SummarizedExperiment-class.html">dim-method</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">dimnames-method</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">dimnames&lt;--method</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">disjoin-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">disjointBins-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">distance-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GenomicRanges-comparison.html">duplicated-method</a></td>
<td>Comparing and ordering genomic ranges</td></tr>
</table>

<h2><a name="E">-- E --</a></h2>

<table width="100%">
<tr><td width="25%"><a href="GRanges-class.html">elementMetadata-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">elementMetadata-method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">elementMetadata-method</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">elementMetadata-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">elementMetadata&lt;--method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">elementMetadata&lt;--method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">elementMetadata&lt;--method</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">elementMetadata&lt;--method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="encodeOverlaps-methods.html">encodeOverlaps-method</a></td>
<td>encodeOverlaps methods and related utilities</td></tr>
<tr><td width="25%"><a href="encodeOverlaps-methods.html">encodeOverlaps-methods</a></td>
<td>encodeOverlaps methods and related utilities</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">end-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">end-method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">end-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">end&lt;--method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">end&lt;--method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">exptData</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">exptData-method</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">exptData&lt;-</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">exptData&lt;--method</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="encodeOverlaps-methods.html">extractSkippedExonRanks</a></td>
<td>encodeOverlaps methods and related utilities</td></tr>
<tr><td width="25%"><a href="encodeOverlaps-methods.html">extractSkippedExonRanks-method</a></td>
<td>encodeOverlaps methods and related utilities</td></tr>
</table>

<h2><a name="F">-- F --</a></h2>

<table width="100%">
<tr><td width="25%"><a href="findOverlaps-methods.html">findOverlaps-method</a></td>
<td>GRanges, GRangesList, GappedAlignments and GappedAlignmentPairs Interval Overlaps</td></tr>
<tr><td width="25%"><a href="findOverlaps-methods.html">findOverlaps-methods</a></td>
<td>GRanges, GRangesList, GappedAlignments and GappedAlignmentPairs Interval Overlaps</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">first</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">first-method</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">flank-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">flank-method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="encodeOverlaps-methods.html">flipQuery</a></td>
<td>encodeOverlaps methods and related utilities</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">follow-method</a></td>
<td>GRanges objects</td></tr>
</table>

<h2><a name="G">-- G --</a></h2>

<table width="100%">
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">GappedAlignmentPairs</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">GappedAlignmentPairs-class</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">GappedAlignments</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">GappedAlignments-class</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">gaps-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="seqinfo.html">genome</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">genome-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td width="25%"><a href="seqinfo.html">genome-method</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="seqinfo.html">genome&lt;-</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">genome&lt;--method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td width="25%"><a href="seqinfo.html">genome&lt;--method</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">GenomicRanges</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">GenomicRanges-class</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GenomicRanges-comparison.html">GenomicRanges-comparison</a></td>
<td>Comparing and ordering genomic ranges</td></tr>
<tr><td width="25%"><a href="GenomicRangesList-class.html">GenomicRangesList</a></td>
<td>GenomicRangesList objects</td></tr>
<tr><td width="25%"><a href="GenomicRangesList-class.html">GenomicRangesList-class</a></td>
<td>GenomicRangesList objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">GenomicRangesORGRangesList-class</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">GenomicRangesORmissing-class</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">GRanges</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">granges</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">GRanges-class</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">granges-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="map-methods.html">granges-method</a></td>
<td>Mapping ranges between sequences</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">GRangesList</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">GRangesList-class</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">grg</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">grglist</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">grglist-method</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">grglist-method</a></td>
<td>GappedAlignments objects</td></tr>
</table>

<h2><a name="I">-- I --</a></h2>

<table width="100%">
<tr><td width="25%"><a href="setops-methods.html">intersect-method</a></td>
<td>Set operations on GRanges/GRangesList/GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="summarizeOverlaps.html">IntersectionNotEmpty</a></td>
<td>Count reads that map to genomic features</td></tr>
<tr><td width="25%"><a href="summarizeOverlaps.html">IntersectionStrict</a></td>
<td>Count reads that map to genomic features</td></tr>
<tr><td width="25%"><a href="seqinfo.html">isCircular</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">isCircular-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td width="25%"><a href="seqinfo.html">isCircular-method</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="seqinfo.html">isCircular&lt;-</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">isCircular&lt;--method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td width="25%"><a href="seqinfo.html">isCircular&lt;--method</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="encodeOverlaps-methods.html">isCompatibleWithSkippedExons</a></td>
<td>encodeOverlaps methods and related utilities</td></tr>
<tr><td width="25%"><a href="encodeOverlaps-methods.html">isCompatibleWithSkippedExons-method</a></td>
<td>encodeOverlaps methods and related utilities</td></tr>
<tr><td width="25%"><a href="encodeOverlaps-methods.html">isCompatibleWithSplicing</a></td>
<td>encodeOverlaps methods and related utilities</td></tr>
<tr><td width="25%"><a href="encodeOverlaps-methods.html">isCompatibleWithSplicing-method</a></td>
<td>encodeOverlaps methods and related utilities</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">isDisjoint-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">isDisjoint-method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">isProperPair</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">isProperPair-method</a></td>
<td>GappedAlignmentPairs objects</td></tr>
</table>

<h2><a name="K">-- K --</a></h2>

<table width="100%">
<tr><td width="25%"><a href="seqlevels-utils.html">keepSeqlevels</a></td>
<td>seqlevels utility functions</td></tr>
<tr><td width="25%"><a href="seqlevels-utils.html">keepSeqlevels-method</a></td>
<td>seqlevels utility functions</td></tr>
</table>

<h2><a name="L">-- L --</a></h2>

<table width="100%">
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">last</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">last-method</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">left</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">left-method</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">length-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">length-method</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">length-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">length-method</a></td>
<td>Seqinfo objects</td></tr>
</table>

<h2><a name="M">-- M --</a></h2>

<table width="100%">
<tr><td width="25%"><a href="GRangesList-class.html">makeGRangesListFromFeatureFragments</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="map-methods.html">map-method</a></td>
<td>Mapping ranges between sequences</td></tr>
<tr><td width="25%"><a href="findOverlaps-methods.html">match-method</a></td>
<td>GRanges, GRangesList, GappedAlignments and GappedAlignmentPairs Interval Overlaps</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">merge-method</a></td>
<td>Seqinfo objects</td></tr>
</table>

<h2><a name="N">-- N --</a></h2>

<table width="100%">
<tr><td width="25%"><a href="GRanges-class.html">names-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">names-method</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">names-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">names-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">names&lt;--method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">names&lt;--method</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">names&lt;--method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">names&lt;--method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">narrow-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">nearest-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">ngap-method</a></td>
<td>GappedAlignments objects</td></tr>
</table>

<h2><a name="O">-- O --</a></h2>

<table width="100%">
<tr><td width="25%"><a href="GenomicRanges-comparison.html">order-method</a></td>
<td>Comparing and ordering genomic ranges</td></tr>
</table>

<h2><a name="P">-- P --</a></h2>

<table width="100%">
<tr><td width="25%"><a href="setops-methods.html">pgap-method</a></td>
<td>Set operations on GRanges/GRangesList/GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="setops-methods.html">pintersect-method</a></td>
<td>Set operations on GRanges/GRangesList/GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">precede-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="setops-methods.html">psetdiff-method</a></td>
<td>Set operations on GRanges/GRangesList/GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="setops-methods.html">punion-method</a></td>
<td>Set operations on GRanges/GRangesList/GappedAlignments objects</td></tr>
</table>

<h2><a name="Q">-- Q --</a></h2>

<table width="100%">
<tr><td width="25%"><a href="GappedAlignments-class.html">qnarrow</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">qnarrow-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="cigar-utils.html">queryLoc2refLoc</a></td>
<td>CIGAR utility functions</td></tr>
<tr><td width="25%"><a href="cigar-utils.html">queryLocs2refLocs</a></td>
<td>CIGAR utility functions</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">qwidth</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">qwidth-method</a></td>
<td>GappedAlignments objects</td></tr>
</table>

<h2><a name="R">-- R --</a></h2>

<table width="100%">
<tr><td width="25%"><a href="GRanges-class.html">range-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">range-method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">ranges-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">ranges-method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">ranges-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">ranges&lt;--method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">ranges&lt;--method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GenomicRanges-comparison.html">rank-method</a></td>
<td>Comparing and ordering genomic ranges</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">readGappedAlignmentPairs</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">readGappedAlignments</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">reduce-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">reduce-method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="seqlevels-utils.html">renameSeqlevels</a></td>
<td>seqlevels utility functions</td></tr>
<tr><td width="25%"><a href="seqlevels-utils.html">renameSeqlevels-method</a></td>
<td>seqlevels utility functions</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">resize-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">restrict-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">restrict-method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">rglist</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">rglist-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">right</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">right-method</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">rname</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">rname-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">rname&lt;-</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">rname&lt;--method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">rowData</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">rowData-method</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">rowData&lt;-</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">rowData&lt;--method</a></td>
<td>SummarizedExperiment instances</td></tr>
</table>

<h2><a name="S">-- S --</a></h2>

<table width="100%">
<tr><td width="25%"><a href="GRanges-class.html">score-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">score-method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="encodeOverlaps-methods.html">selectEncodingWithCompatibleStrand</a></td>
<td>encodeOverlaps methods and related utilities</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">Seqinfo</a></td>
<td>Seqinfo objects</td></tr>
<tr><td width="25%"><a href="seqinfo.html">seqinfo</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">Seqinfo-class</a></td>
<td>Seqinfo objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">seqinfo-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">seqinfo-method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">seqinfo-method</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">seqinfo-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="seqinfo.html">seqinfo-method</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="seqinfo.html">seqinfo&lt;-</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">seqinfo&lt;--method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">seqinfo&lt;--method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">seqinfo&lt;--method</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">seqinfo&lt;--method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="seqinfo.html">seqinfo&lt;--method</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="seqinfo.html">seqlengths</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">seqlengths-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td width="25%"><a href="seqinfo.html">seqlengths-method</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="seqinfo.html">seqlengths&lt;-</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">seqlengths&lt;--method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td width="25%"><a href="seqinfo.html">seqlengths&lt;--method</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="seqinfo.html">seqlevels</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">seqlevels-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td width="25%"><a href="seqinfo.html">seqlevels-method</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="seqinfo.html">seqlevels&lt;-</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">seqlevels&lt;--method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td width="25%"><a href="seqinfo.html">seqlevels&lt;--method</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="seqinfo.html">seqnames</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">seqnames-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">seqnames-method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">seqnames-method</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">seqnames-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">seqnames-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td width="25%"><a href="seqinfo.html">seqnames-method</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="seqinfo.html">seqnames&lt;-</a></td>
<td>Accessing sequence information</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">seqnames&lt;--method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">seqnames&lt;--method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">seqnames&lt;--method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">seqnames&lt;--method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">seqselect-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">seqselect&lt;--method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="setops-methods.html">setdiff-method</a></td>
<td>Set operations on GRanges/GRangesList/GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="setops-methods.html">setops-methods</a></td>
<td>Set operations on GRanges/GRangesList/GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">shift-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">shift-method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">show-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">show-method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">show-method</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">show-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">show-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">show-method</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="GenomicRangesList-class.html">SimpleGenomicRangesList-class</a></td>
<td>GenomicRangesList objects</td></tr>
<tr><td width="25%"><a href="GenomicRanges-comparison.html">sort-method</a></td>
<td>Comparing and ordering genomic ranges</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">split-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="cigar-utils.html">splitCigar</a></td>
<td>CIGAR utility functions</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">start-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">start-method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">start-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">start&lt;--method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">start&lt;--method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">strand-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">strand-method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">strand-method</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">strand-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="strand-utils.html">strand-method</a></td>
<td>Strand utilities</td></tr>
<tr><td width="25%"><a href="strand-utils.html">strand-utils</a></td>
<td>Strand utilities</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">strand&lt;--method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">strand&lt;--method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">strand&lt;--method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="strand-utils.html">strand&lt;--method</a></td>
<td>Strand utilities</td></tr>
<tr><td width="25%"><a href="findOverlaps-methods.html">subsetByOverlaps-method</a></td>
<td>GRanges, GRangesList, GappedAlignments and GappedAlignmentPairs Interval Overlaps</td></tr>
<tr><td width="25%"><a href="cigar-utils.html">summarizeCigarTable</a></td>
<td>CIGAR utility functions</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">SummarizedExperiment</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">SummarizedExperiment-class</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">SummarizedExperiment-method</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="summarizeOverlaps.html">summarizeOverlaps</a></td>
<td>Count reads that map to genomic features</td></tr>
<tr><td width="25%"><a href="summarizeOverlaps.html">summarizeOverlaps-method</a></td>
<td>Count reads that map to genomic features</td></tr>
</table>

<h2><a name="U">-- U --</a></h2>

<table width="100%">
<tr><td width="25%"><a href="summarizeOverlaps.html">Union</a></td>
<td>Count reads that map to genomic features</td></tr>
<tr><td width="25%"><a href="setops-methods.html">union-method</a></td>
<td>Set operations on GRanges/GRangesList/GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GenomicRanges-comparison.html">unique-method</a></td>
<td>Comparing and ordering genomic ranges</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">unlist-method</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">updateObject-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">updateObject-method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">updateObject-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">updateObject-method</a></td>
<td>Seqinfo objects</td></tr>
</table>

<h2><a name="V">-- V --</a></h2>

<table width="100%">
<tr><td width="25%"><a href="cigar-utils.html">validCigar</a></td>
<td>CIGAR utility functions</td></tr>
</table>

<h2><a name="W">-- W --</a></h2>

<table width="100%">
<tr><td width="25%"><a href="GRanges-class.html">width-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">width-method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">width-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">width&lt;--method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">width&lt;--method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">window-method</a></td>
<td>GRanges objects</td></tr>
</table>

<h2><a name="misc">-- misc --</a></h2>

<table width="100%">
<tr><td width="25%"><a href="SummarizedExperiment-class.html">$-method</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">$&lt;--method</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="findOverlaps-methods.html">%in%-method</a></td>
<td>GRanges, GRangesList, GappedAlignments and GappedAlignmentPairs Interval Overlaps</td></tr>
<tr><td width="25%"><a href="GenomicRanges-comparison.html">&lt;-method</a></td>
<td>Comparing and ordering genomic ranges</td></tr>
<tr><td width="25%"><a href="GenomicRanges-comparison.html">&lt;=-method</a></td>
<td>Comparing and ordering genomic ranges</td></tr>
<tr><td width="25%"><a href="GenomicRanges-comparison.html">==-method</a></td>
<td>Comparing and ordering genomic ranges</td></tr>
<tr><td width="25%"><a href="GenomicRanges-comparison.html">&gt;-method</a></td>
<td>Comparing and ordering genomic ranges</td></tr>
<tr><td width="25%"><a href="GenomicRanges-comparison.html">&gt;=-method</a></td>
<td>Comparing and ordering genomic ranges</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">[-method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">[-method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">[-method</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="GappedAlignments-class.html">[-method</a></td>
<td>GappedAlignments objects</td></tr>
<tr><td width="25%"><a href="Seqinfo-class.html">[-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">[-method</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="GRanges-class.html">[&lt;--method</a></td>
<td>GRanges objects</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">[&lt;--method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">[&lt;--method</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="GappedAlignmentPairs-class.html">[[-method</a></td>
<td>GappedAlignmentPairs objects</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">[[-method</a></td>
<td>SummarizedExperiment instances</td></tr>
<tr><td width="25%"><a href="GRangesList-class.html">[[&lt;--method</a></td>
<td>GRangesList objects</td></tr>
<tr><td width="25%"><a href="SummarizedExperiment-class.html">[[&lt;--method</a></td>
<td>SummarizedExperiment instances</td></tr>
</table>
</body></html>
